The evolution of gene regulation by transcription factors and microRNAs (original) (raw)
Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature424, 147–151 (2003). ArticleCASPubMed Google Scholar
Moore, M. J. From birth to death: the complex lives of eukaryotic mRNAs. Science309, 1514–1518 (2005). ArticleCASPubMed Google Scholar
Davidson, E. H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic, New York, 2006). This book synthesizes several decades of work on gene regulation, animal development and evolution, with an emphasis on transcriptional regulation. Google Scholar
Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism and function. Cell116, 281–297 (2004). ArticleCASPubMed Google Scholar
Wittkopp, P. J. Genomic sources of regulatory variation in cis and in trans. Cell. Mol. Life Sci.62, 1779–1783 (2005). ArticleCASPubMed Google Scholar
Davidson, E. H. & Erwin, D. H. Gene regulatory networks and the evolution of animal body plans. Science311, 796–800 (2006). ArticleCASPubMed Google Scholar
Carroll, S., Grenier, J. & Weatherbee, S. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (Blackwell Scientific, Malden, 2005). Google Scholar
Kloosterman, W. P. & Plasterk, R. H. The diverse functions of microRNAs in animal development and disease. Dev. Cell11, 441–450 (2006). ArticleCASPubMed Google Scholar
Kosik, K. S. The neuronal microRNA system. Nature Rev. Neurosci.7, 911–920 (2006). ArticleCAS Google Scholar
Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science301, 336–338 (2003). ArticleCASPubMed Google Scholar
Jones-Rhoades, M. W., Bartel, D. P. & Bartel, B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol.57, 19–53 (2006). ArticleCASPubMed Google Scholar
Alvarez-Garcia, I. & Miska, E. A. MicroRNA functions in animal development and human disease. Development132, 4653–4662 (2005). ArticleCASPubMed Google Scholar
Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75, 843–854 (1993). ArticleCASPubMed Google Scholar
Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature403, 901–906 (2000). ArticleCASPubMed Google Scholar
Sokol, N. S. & Ambros, V. Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev.19, 2343–2354 (2005). ArticleCASPubMedPubMed Central Google Scholar
Giraldez, A. J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science312, 75–79 (2006). ArticleCASPubMed Google Scholar
Giraldez, A. J., Cinalli, R. M., Glasner, M. E., Thomson, J. M. & Baskerville, S. MicroRNAs regulate brain morphogenesis in zebrafish. Science308, 833–838 (2005). ArticleCASPubMed Google Scholar
Bernstein, E. et al. Dicer is essential for mouse development. Nature Genet.35, 215–217 (2003). ArticleCASPubMed Google Scholar
Schauer, S. E., Jacobsen, S. E., Meinke, D. W. & Ray, A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci.7, 487–491 (2002). ArticleCASPubMed Google Scholar
Wienholds, E. et al. MicroRNA expression in zebrafish embryonic development. Science309, 310–311 (2005). ArticleCASPubMed Google Scholar
Thomson, J. M. et al. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev.20, 2202–2207 (2006). ArticleCASPubMedPubMed Central Google Scholar
Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell5, 337–350 (2003). ArticleCASPubMed Google Scholar
Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M. & Lai, E. C. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc. Natl Acad. Sci. USA102, 18017–18022 (2005). ArticleCASPubMedPubMed Central Google Scholar
Leaman, D. et al. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell121, 1097–1108 (2005). ArticleCASPubMed Google Scholar
Brennecke, J., Stark, A. & Cohen, S. M. Not miR-ly muscular: microRNAs and muscle development. Genes Dev.19, 2261–2264 (2005). ArticleCASPubMed Google Scholar
Hornstein, E. & Shomron, S. Canalization of development by microRNAs. Nature Genet.38, S20–S24 (2006). ArticleCASPubMed Google Scholar
Li, Y., Wang, Y., Lee, J. A. & Gao, F. B. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev.20, 2793–2805 (2006). ArticleCASPubMedPubMed Central Google Scholar
Cohen S. M., Brennecke, J. & Stark A. Denoising feedback loops by thresholding — a new role for microRNAs. Genes Dev.20, 2769–2772 (2006). ArticleCASPubMed Google Scholar
Meyerowitz, E. M. Plants compared to animals: the broadest comparative study of development. Science295, 1482–1485 (2002). ArticleCASPubMed Google Scholar
Riechmann, J. L. et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science290, 2105–2110 (2000). A detailed study of the evolution of transcription- factor families in plants and animals, which showed that they have diversified greatly during eukaryotic evolution. ArticleCASPubMed Google Scholar
Hsia, C. C. & McGinnis, W. Evolution of transcription factor function. Curr. Opin. Genet. Dev.13, 199–206 (2003). ArticleCASPubMed Google Scholar
Pasquinelli, A. E. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature408, 86–89 (2000). This paper demonstrated thatlet-7, one of the two founding miRNAs, is highly conserved in animals. ArticleCASPubMed Google Scholar
Pasquinelli, A. E. et al. Expression of the 22 nucleotide let-7 heterochronic RNA throughout the metazoa: a role in life history evolution? Evol. Dev.5, 372–378 (2003). ArticleCASPubMed Google Scholar
Sempere, L. F., Cole, C. N., McPeek, M. A. & Peterson, K. J. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. B. Mol. Dev. Evol.306, 575–588 (2006). The authors studied the evolution of miRNAs in bilaterians, cnidarians and sponges, and proposed that the acquisition of new miRNAs has had an important role in the development of new animal organs. ArticlePubMedCAS Google Scholar
Prochnik, S. E., Rokhsar, D. S. & Aboobaker, A. A. Evidence for a microRNA expansion in the bilaterian ancestor. Dev. Genes Evol. 14 Nov 2006 (doi: 10.1007/s00427-006-0116-1). ArticlePubMedCAS Google Scholar
Lemons, D. & McGinnis, W. Genomic evolution of Hox gene clusters. Science313, 1918–1922 (2006). ArticleCASPubMed Google Scholar
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature434, 338–345 (2005). ArticleCASPubMedPubMed Central Google Scholar
Chen, K. & Rajewsky, N. Deep conservation of miRNA-target relationships and 3′ UTR motifs in vertebrates, flies and nematodes. Cold Spring Harb. Symp. Quant. Biol. 12 Dec 2006 (doi:10.1101/sqb.2006.71.039). ArticleCASPubMed Google Scholar
Chan, C. S., Elemento, O. & Tavazoie, S. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput. Biol.1, e69 (2006). ArticleCAS Google Scholar
Lu, C. et al. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res.16, 1276–1288 (2006). ArticleCASPubMedPubMed Central Google Scholar
Arazi, T. et al. Cloning and characterization of micro-RNAs from moss. Plant J.43, 837–848 (2005). ArticleCASPubMed Google Scholar
Floyd, S. K. & Bowman, J. L. Gene regulation: ancient microRNA target sequences in plants. Nature428, 485–486 (2004). ArticleCASPubMed Google Scholar
Axtell, M. J. & Bartel, D. P. Antiquity of microRNAs and their targets in land plants. Plant Cell17, 1658–1673 (2005). These authors showed that many miRNAs and miRNA-target relationships are well conserved in plants. ArticleCASPubMedPubMed Central Google Scholar
Shiu, S. H., Shih, M. C. & Li, W. H. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol.139, 18–26 (2005). ArticleCASPubMedPubMed Central Google Scholar
Blanc, G. & Wolfe, K. H. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell16, 1679–1691 (2004). ArticleCASPubMedPubMed Central Google Scholar
Seoighe, C. & Gehring, C. Genome duplication led to highly selective expansion of the Arabidopsis thaliana promoterome. Trends Genet.20, 461–464 (2004). ArticleCASPubMed Google Scholar
Davis, J. C. & Petrov, D. A. Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet.21, 548–551 (2005). ArticleCASPubMed Google Scholar
Tanzer, A., Amemiya, C. T., Kim, C. B. & Stadler, P. F. Evolution of microRNAs located within Hox gene clusters. J. Exp. Zool. B. Mol. Dev. Evol.304, 75–85 (2005). ArticlePubMedCAS Google Scholar
Tanzer, A. & Stadler, P. F. Molecular evolution of a microRNA cluster. J. Mol. Biol.339, 327–335 (2004). ArticleCASPubMed Google Scholar
Li, A. & Mao, L. Evolution of plant microRNA gene families. Cell Res. 28 Nov 2006 (doi:10.1038/sj.cr.7310113). ArticleCAS Google Scholar
Abbott, A. L. et al. The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev. Cell9, 403–414 (2005). ArticleCASPubMedPubMed Central Google Scholar
Hayes, G. D., Frand, A. R. & Ruvkun, G. The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25. Development133, 4631–4641 (2006). ArticleCASPubMed Google Scholar
Johnson, R. M. et al. RAS is regulated by the let-7 microRNA family. Cell120, 635–647 (2005). ArticleCASPubMed Google Scholar
Schulman, B. R. M., Esquela-Kerscher, A. & Slack, F. J. Reciprocal expression of L in-41 and the microRNAs L et-7 and M ir-125 during mouse embryogenesis. Dev. Dyn.234, 1046–1054 (2005). ArticleCASPubMedPubMed Central Google Scholar
Moss, E. G. & Tang, L. Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. Dev. Biol.258, 432–442 (2003). ArticleCASPubMed Google Scholar
Yang, D.-H. & Moss, E. G. Temporally regulated expression of Lin-28 in diverse tissues of the developing mouse. Gene Expr. Patterns3, 719–726 (2003). ArticleCASPubMed Google Scholar
Grun, D., Wang, Y., Langenberger, D., Gunsalus, K. C. & Rajewsky, N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol.1, e13 (2005). ArticlePubMedPubMed CentralCAS Google Scholar
Elnitski, L., Jin, V. X., Farnham, P. J. & Jones, S. J. M. Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques Genome Res.16, 1455–1464 (2006). ArticleCASPubMed Google Scholar
Gerber, A. P., Luschnig, S., Krasnow, M. A., Brown, P. O. & Herschlag, D. Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc. Natl Acad. Sci. USA103, 4487–4492 (2006). ArticleCASPubMedPubMed Central Google Scholar
Dermitzakis, E. T. & Clark, A. G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol.19, 1114–1121 (2002). ArticleCASPubMed Google Scholar
Dermitzakis, E. T., Bergman, C. M. & Clark, A. G. Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol. Biol. Evol.20, 703–714 (2003). ArticleCASPubMed Google Scholar
Emberly, E., Rajewsky, N. & Siggia, E. D. Conservation of regulatory elements between two regions of Drosophila. BMC Bioinformatics4, 57 (2003). ArticlePubMedPubMed Central Google Scholar
Richards, S. et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene and _cis_-element conservation. Genome Res.15, 1–18 (2005). ArticleCASPubMedPubMed Central Google Scholar
Moses, A. M. et al. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput. Biol.2, e130 (2006). ArticlePubMedPubMed CentralCAS Google Scholar
Ludwig, M. Z., Bergman, C. M., Patel, N. H. & Kreitman, M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature403, 564–567 (2000). An elegant demonstration of the complex evolution of the well studiedD. melanogastereven-skipped stripe 2 enhancer. ArticleCASPubMed Google Scholar
Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature438, 685–689 (2005). ArticlePubMedCAS Google Scholar
Sood, P., Krek, A., Zavolan, M., Macino, G. & Rajewsky, N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl Acad. Sci. USA103, 2746–2751 (2006). ArticleCASPubMedPubMed Central Google Scholar
Chen, K. & Rajewsky, N. Natural selection on human miRNA binding sites inferred from SNP data. Nature Genet.38, 1452–1456 (2006). This paper examined polymorphism in human miRNA binding sites and used population genetic techniques to estimate levels of selective constraint on these binding sites. ArticleCASPubMed Google Scholar
Rockman, M. V. & Wray, G. A. Abundant raw material for _cis_-reguatory evolution in humans. Mol. Biol. Evol.19, 1991–2004 (2002). A systematic survey of the literature on naturally occurring polymorphisms in human promoter regions that significantly affect gene expression levels. ArticleCASPubMed Google Scholar
Abelson, J. F. et al. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science310, 317–320 (2005). ArticleCASPubMed Google Scholar
Clop, A. et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genet.38, 813–818 (2006). The clearest example to date of a naturally occurring SNP in a miRNA binding site that affects a gross phenotypic trait. ArticleCASPubMed Google Scholar
Iwai, N. & Naraba, H. Polymorphisms in human pre-miRNAs. Biochem. Biophys. Res. Commun.331, 1439–1444 (2005). ArticleCASPubMed Google Scholar
Wray, G. A. et al. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol.20, 1377–1419 (2003). A comprehensive review of the evolution of transcription factors and their binding sites. ArticleCASPubMed Google Scholar
Balhoff, J. P. & Wray, G. A. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proc. Natl Acad. Sci. USA102, 8591–8596 (2005). ArticleCASPubMedPubMed Central Google Scholar
Sinha, S. & Siggia, E. D. Sequence turnover and tandem repeats in _cis_-regulatory modules in Drosophila. Mol. Biol. Evol.22, 874–885 (2005). ArticleCASPubMed Google Scholar
Stone, J. & Wray, G. Rapid evolution of _cis_-regulatory sequences via local point mutations. Mol. Biol. Evol.18, 1764–1770 (2001). ArticleCASPubMed Google Scholar
MacArthur, S. & Brookfield, J. F. Y. Expected rates and modes of evolution of enhancer sequences. Mol. Biol. Evol.21, 1064–1073 (2004). ArticleCASPubMed Google Scholar
Durrett, R. & Schmidt, D. Waiting for regulatory sequences to appear. Ann. Appl. Probab. (in the press).
Berezikov, E. et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res.16, 1289–1298 (2006). ArticleCASPubMedPubMed Central Google Scholar
Berezikov, E. et al. Diversity of microRNAs in human and chimpanzee brain. Nature Genet.38, 1375–1377 (2006). These authors used 454 sequencing to show that many miRNAs that are expressed in the human brain are not conserved in the chimpanzee brain. ArticleCASPubMed Google Scholar
Schwab, R. et al. Specific effects on microRNAs on the plant transcriptome. Dev. Cell8, 517–527 (2005). ArticleCASPubMed Google Scholar
Allen, E. et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genet.36, 1282–1290 (2004). ArticleCASPubMed Google Scholar
Svoboda, P. & Di Cara, A. Hairpin RNA: a secondary structure of primary importance. Cell. Mol. Life Sci.63, 901–918 (2006). ArticleCASPubMed Google Scholar
Bentwich, I. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genet.37, 766–770 (2005). ArticleCASPubMed Google Scholar
Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet.5, 396–400 (2004). ArticleCASPubMed Google Scholar
Farh, K. K. et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science310, 1817–1821 (2005). ArticleCASPubMed Google Scholar
Stark, A., Brennecke, J., Bushati, N., Russell, R. B. & Cohen, S. M. Animal microRNAs confer robustness to gene expression and have a significant impact on 3′ UTR evolution. Cell123, 1133–1146 (2005). ArticleCASPubMed Google Scholar
Baskerville, S. & Bartel, D. P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA11, 241–247 (2005). ArticleCASPubMedPubMed Central Google Scholar
Bhattacharyya, S. N., Habermacher, R., Martine, U., Closs, E. I. & Filipowicz, W. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell125, 1111–1124 (2006). ArticleCASPubMed Google Scholar
Ashraf, S. I., McLoon, A. L., Sclarsic, S. M. & Kunes, S. Synaptic protein synthesis associated with memory is regulated by the RISC pathway in Drosophila. Cell124, 191–205 (2006). ArticleCASPubMed Google Scholar
Davidson, E. H. Genomic Regulatory Systems. Development and Evolution (Academic, San Diego, 2001). Google Scholar
Johnston, R. J. J., Chang, S., Etchberger, J. F., Ortiz, C. O. & Hobert, O. MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl Acad. Sci.102, 12449–12454 (2005). ArticleCASPubMedPubMed Central Google Scholar
Yoo, A. S. & Greenwald, I. LIN-12/Notch activation leads to microRNA-mediated down-regulation of Vav in C. elegans. Science310, 1330–1333 (2005). ArticleCASPubMedPubMed Central Google Scholar
Fazi, F. et al. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPa regulates human granulopoiesis. Cell123, 819–831 (2005). ArticleCASPubMed Google Scholar
King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science188, 107–116 (1975). ArticleCASPubMed Google Scholar
Johnson, S. M., Lin, S. Y. & Slack, F. J. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev. Biol.259, 364–379 (2003). ArticleCASPubMed Google Scholar
Biemar, F. et al. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc. Natl Acad. Sci.102, 15907–15911 (2005). ArticleCASPubMedPubMed Central Google Scholar
Engels, B. M. & Hutvagner, G. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene25, 6163–6169 (2006). ArticleCASPubMed Google Scholar
Berezikov, E., Cuppen, E. & Plasterk, R. H. Approaches to microRNA discovery. Nature Genet.38, S2–S7 (2006). ArticleCASPubMed Google Scholar
Bentwich, I. Prediction and validation of microRNAs and their targets. FEBS Lett.579, 5904–5910 (2005). ArticleCASPubMed Google Scholar
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science294, 853–858 (2001). ArticleCASPubMed Google Scholar
Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science309, 1567–1569 (2005). ArticleCASPubMed Google Scholar
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. & Eddy, S. R. Rfam: an RNA family database. Nucleic Acids Res.31, 439–441 (2003). ArticleCASPubMedPubMed Central Google Scholar
Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell115, 787–798 (2003). ArticleCASPubMed Google Scholar
Lall, S. et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol.16, 460–471 (2006). ArticleCASPubMed Google Scholar
Sethupathy, P., Megraw, M. & Hatzigeorgiou, A. G. A guide through present computational approaches for the identification of mammalian microRNA targets. Nature Methods3, 881–886 (2006). ArticleCASPubMed Google Scholar
Tompa, M. et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnol.23, 137–144 (2005). ArticleCAS Google Scholar
Siggia, E. D. Computational methods for transcriptional regulation. Curr. Opin. Genet. Dev.15, 214–221 (2005). ArticleCASPubMed Google Scholar
Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature433, 769–773 (2005). ArticleCASPubMed Google Scholar
Pillai, R. S., Bhattacharyya, S. N. & Filipowicz, W. Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol. 2 Jan 2007 (doi:10.1016/j.tcb.2006.12.007). ArticleCASPubMed Google Scholar
Arteaga-Vazquez, M., Caballero-Perez, J. & Vielle-Calzada, J. P. A family of microRNAs present in plants and animals. Plant Cell 22 Dec 2006 (doi:10.1105/tpc.106.044420). ArticleCAS Google Scholar
Rajagopalan, R., Vaucheret, H., Trejo, J., Bartel, D. P. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev.20, 3407–3425. ArticleCAS Google Scholar